I am putting a ls1 out of a vx commodore in my car and also have similar problems with th built in security on modern cars . At the moment i now of two ways you can fix it . One is to trow away you wiring ang computer and get an aftermarket kit fitted such as a Motec or Wolf 3d and the other is to contact the link bellow and they should be able to make you a new loom and reprogram your ecu to ignore the security part as they can do it for my ls1 at a cost of about 1g . Hope this helps.
http://www.castleauto.com.au/